I have been searching for the last day to try to find a solution without having to create a post, but alas! From everything I've read the BRPs make a lot of noise, I'm cool with that as long as its normal so here it is:

I just traded my street bike for a 01xr650 It has less than 8k miles and the previous owner claims he changed the oil and checked the valve clearance every 600 miles. I rode it 70 miles back home and on the way home I noticed it started making a knocking/clicking noise in lower rpms. When I got home i inspected further and noticed that the engine sounds fine at idle and at higher rpms but when you start to put load on it you hear it clicking, or if you're just chugging along at low rpm you can hear it. I changed the oil and it didn't solve the problem. Is it the cam chain? It doesn't seem to be clutch chatter as it doesn't do it at idle. There is no hesitation and it has plenty of power so I don't suspect valve clearance, though I could be wrong.

ALSO I when I got it out today to start it, it would start, make a different clicking sound (sounded like the decompression valve) and shut off as if the valve was getting stuck.How do I fix this?

The clicking noise could be the final drive chain rattling. Dirt bikes have more play in the chain than road bikes and often make this noise. If you are new to dirt bikes you would not have heard the noise before.With regards to the stalling check the decompression cable for free play especially at full lock.